User contributions
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Jump to navigationJump to search- 22:13, 17 November 2010 diff hist -465 Software Undo revision 2523 by Upugema (Talk)
- 16:21, 17 November 2010 diff hist -22 LibStatGen: GLF
- 16:20, 17 November 2010 diff hist -22 LibStatGen: FASTQ
- 16:20, 17 November 2010 diff hist -22 C++ Class: FastQFile
- 16:18, 17 November 2010 diff hist -22 C++ Class: SamRecord
- 16:18, 17 November 2010 diff hist -22 C++ Class: SamFileHeader
- 16:16, 17 November 2010 diff hist -22 C++ Class: SamFile
- 16:16, 17 November 2010 diff hist -22 LibStatGen: BAM
- 16:15, 17 November 2010 diff hist -22 C++ Class: CigarRoller
- 16:14, 17 November 2010 diff hist -22 C++ Class: InputFile
- 16:14, 17 November 2010 diff hist -22 LibStatGen: general
- 16:13, 17 November 2010 diff hist +10 C++ Library: libStatGen
- 14:41, 17 November 2010 diff hist +31 LibStatGen Download
- 14:35, 17 November 2010 diff hist +26 FastQValidator
- 14:33, 17 November 2010 diff hist +411 FastQValidator
- 14:32, 17 November 2010 diff hist 0 File:StatGen.0.1.2.tgz uploaded a new version of "File:StatGen.0.1.2.tgz": Quick fix to update the usage for fastqValidator current
- 14:24, 17 November 2010 diff hist 0 File:StatGen.0.1.2.tgz uploaded a new version of "File:StatGen.0.1.2.tgz"
- 14:20, 17 November 2010 diff hist 0 N File:StatGen.0.1.2.tgz
- 14:19, 17 November 2010 diff hist +94 LibStatGen Download
- 14:17, 17 November 2010 diff hist -119 LibStatGen Download
- 14:17, 17 November 2010 diff hist 0 LibStatGen Download
- 14:17, 17 November 2010 diff hist +854 LibStatGen Download
- 17:19, 12 November 2010 diff hist +81 C++ Library: libStatGen
- 17:11, 12 November 2010 diff hist +210 LibStatGen: GLF
- 16:50, 12 November 2010 diff hist -2 LibStatGen: GLF
- 16:49, 12 November 2010 diff hist +44 LibStatGen: GLF
- 12:07, 12 November 2010 diff hist +49 Software
- 13:46, 9 November 2010 diff hist -112 LibStatGen Download
- 13:00, 9 November 2010 diff hist 0 N File:StatGen.0.1.1.tgz current
- 12:59, 9 November 2010 diff hist +196 LibStatGen Download
- 14:14, 8 November 2010 diff hist -1 Software
- 14:14, 8 November 2010 diff hist +18 Software
- 14:13, 8 November 2010 diff hist +94 Software
- 14:12, 8 November 2010 diff hist 0 N File:TrostASHG2010.pdf current
- 13:27, 8 November 2010 diff hist +64 LibStatGen Download
- 12:58, 8 November 2010 diff hist +544 N LibStatGen Download Created page with ' == Download == Click the link to download the tar of the statgen library and tools: StatGen.0.1.0.tgz '''If you use this software, please e-mail me,…'
- 12:56, 8 November 2010 diff hist -325 Software
- 02:37, 2 November 2010 diff hist +37 LibStatGen: GLF
- 02:23, 2 November 2010 diff hist +31 N Category:LibStatGen GLF Created page with 'StatGen classes relating to GLF' current
- 02:22, 2 November 2010 diff hist -3 LibStatGen: BAM
- 02:21, 2 November 2010 diff hist +1,253 N LibStatGen: GLF Created page with 'Category:Software Category:C++ Category:libStatGen Category:libStatGen GLF = GLF = === GLF Classes === {| style="margin: 1em 1em 1em 0; background-color: #f9f9f…'
- 02:16, 2 November 2010 diff hist +1 C++ Library: libStatGen
- 02:15, 2 November 2010 diff hist +198 C++ Library: libStatGen →Download
- 02:13, 2 November 2010 diff hist 0 N File:StatGen.0.1.0.tgz current
- 02:11, 2 November 2010 diff hist -26 BamUtil: validate
- 02:11, 2 November 2010 diff hist -13 BamUtil
- 02:10, 2 November 2010 diff hist +40 Software
- 02:08, 2 November 2010 diff hist 0 BamUtil
- 02:07, 2 November 2010 diff hist -13 BamUtil
- 02:06, 2 November 2010 diff hist +44 BamUtil
- 02:05, 2 November 2010 diff hist +28 BamUtil: validate
- 02:04, 2 November 2010 diff hist -349 BamUtil: validate
- 02:03, 2 November 2010 diff hist +347 Software
- 02:00, 2 November 2010 diff hist +54 C++ Class: CigarRoller
- 01:59, 2 November 2010 diff hist 0 N File:StatGen 0.1.0.tgz current
- 01:58, 2 November 2010 diff hist +58 C++ Class: InputFile
- 01:56, 2 November 2010 diff hist +52 N Category:LibStatGen general Created page with 'part of the general directory of the statgen library' current
- 01:56, 2 November 2010 diff hist +57 C++ Library: general Change Log
- 01:56, 2 November 2010 diff hist +52 C++ Library: general Change Log
- 01:55, 2 November 2010 diff hist +45 N C++ Library: libcsg Change Log moved C++ Library: libcsg Change Log to C++ Library: general Change Log current
- 01:55, 2 November 2010 diff hist 0 m C++ Library: general Change Log moved C++ Library: libcsg Change Log to C++ Library: general Change Log
- 01:55, 2 November 2010 diff hist +76 LibStatGen: general
- 01:53, 2 November 2010 diff hist +37 N C++ Library: libcsg moved C++ Library: libcsg to StatGenLibrary: general current
- 01:53, 2 November 2010 diff hist 0 m LibStatGen: general moved C++ Library: libcsg to StatGenLibrary: general
- 01:50, 2 November 2010 diff hist +68 C++ Class: SamRecord
- 01:50, 2 November 2010 diff hist +68 C++ Class: SamFileHeader
- 01:49, 2 November 2010 diff hist +92 C++ Class: SamFile
- 01:48, 2 November 2010 diff hist +53 Sam Library Usage Examples
- 01:48, 2 November 2010 diff hist +53 SAM/BAM Classes FAQs
- 01:47, 2 November 2010 diff hist +53 BAM Review Action Items
- 01:46, 2 November 2010 diff hist +47 N Category:LibStatGen BAM Created page with 'Part of the BAM portion of the statGen library.' current
- 01:45, 2 November 2010 diff hist +34 N SAM/BAM Library FAQs moved SAM/BAM Library FAQs to SAM/BAM Classes FAQs current
- 01:45, 2 November 2010 diff hist 0 m SAM/BAM Classes FAQs moved SAM/BAM Library FAQs to SAM/BAM Classes FAQs
- 01:44, 2 November 2010 diff hist +27 LibStatGen: BAM
- 01:44, 2 November 2010 diff hist +47 N Category:LibStatGen FASTQ Created page with 'Part of the FASTQ folder of the StatGen Library' current
- 01:43, 2 November 2010 diff hist +94 C++ Class: FastQFile
- 01:43, 2 November 2010 diff hist +55 C++ Library: FASTQ Change Log
- 01:43, 2 November 2010 diff hist +34 N Category:LibStatGen Created page with 'These pages are part of libStatGen' current
- 01:42, 2 November 2010 diff hist +64 C++ Library: libStatGen
- 01:42, 2 November 2010 diff hist +94 LibStatGen: FASTQ
- 01:40, 2 November 2010 diff hist -26 FastQValidator
- 01:34, 2 November 2010 diff hist -361 LibStatGen: BAM
- 01:32, 2 November 2010 diff hist +2 C++ Library: FASTQ Change Log
- 01:32, 2 November 2010 diff hist +50 C++ Library: FASTQ Change Log
- 01:31, 2 November 2010 diff hist -3 LibStatGen: FASTQ →Library Output
- 01:31, 2 November 2010 diff hist +11 LibStatGen: FASTQ
- 01:18, 2 November 2010 diff hist +20 LibStatGen: FASTQ
- 01:17, 2 November 2010 diff hist +43 N C++ Library: libfqf Change Log moved C++ Library: libfqf Change Log to C++ Library: FASTQ Change Log current
- 01:17, 2 November 2010 diff hist 0 m C++ Library: FASTQ Change Log moved C++ Library: libfqf Change Log to C++ Library: FASTQ Change Log
- 01:14, 2 November 2010 diff hist -1 LibStatGen: FASTQ →FastQValidator
- 01:13, 2 November 2010 diff hist -319 LibStatGen: FASTQ
- 01:11, 2 November 2010 diff hist +2,517 Software
- 00:35, 2 November 2010 diff hist +53 VcfGenomeStat current
- 00:19, 2 November 2010 diff hist +1,040 N VcfGenomeStat Created page with '== Purpose == vcfGenomeStat - print flanking sequences and how often they appear for input vcf file. == Usage == <pre> ../bin/vcfGenomeStat [-L <integer>] [-w <integer>] [-l…'
- 18:47, 1 November 2010 diff hist 0 BamUtil: splitBam
- 18:44, 1 November 2010 diff hist +32 BamUtil: splitBam
- 18:39, 1 November 2010 diff hist +876 N BamUtil: splitBam Created page with '== SplitBam == Split a BAM file into multiple BAM files based on ReadGroup according to the following details. # Creates multiple output files named [outprefix].[RGID].bam, for e…'
- 18:37, 1 November 2010 diff hist +79 BamUtil: mergeBam
- 18:31, 1 November 2010 diff hist +4 BamUtil: mergeBam
- 18:30, 1 November 2010 diff hist -4 BamUtil: mergeBam
- 18:29, 1 November 2010 diff hist +10 BamUtil: mergeBam
- 18:29, 1 November 2010 diff hist -65 BamUtil: mergeBam
- 18:29, 1 November 2010 diff hist +359 BamUtil: mergeBam
- 18:05, 1 November 2010 diff hist -1 BamUtil: mergeBam
- 17:42, 1 November 2010 diff hist +70 BamUtil: mergeBam
- 17:40, 1 November 2010 diff hist +796 N BamUtil: mergeBam Created page with ' rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers. * Checks that the HD and SQ tags are identical across the BA…'
- 17:34, 1 November 2010 diff hist +2,840 N Pileup Created page with ' Features: # Option to include a VCF file to select chromosome locations of interest #* Input VCF file can be gzipped or plain text. #*The output VCF file when an input VCF file …'
- 16:21, 1 November 2010 diff hist +3,542 BamUtil: polishBam
- 15:21, 29 October 2010 diff hist -56 BamUtil: polishBam
- 14:47, 29 October 2010 diff hist -52 BamUtil: polishBam
- 14:46, 29 October 2010 diff hist +379 BamUtil: polishBam
- 14:42, 29 October 2010 diff hist +917 N BamUtil: polishBam Created page with '== Trim BAM == The <code>trimBam</code> program is released as part of the StatGen Library & Tools download. <code>trimBam</code> trims the end of reads in a SAM/BAM file, chang…'
- 14:40, 29 October 2010 diff hist +40 N Category:BAM Software Created page with 'Software tools that work with BAM files.'
- 14:40, 29 October 2010 diff hist +26 BamUtil: trimBam
- 14:40, 29 October 2010 diff hist +86 N Category:StatGen Download Created page with 'These are the tools and library classes that are downloaded with the statgen download.' current
- 14:39, 29 October 2010 diff hist +24 BamUtil: trimBam
- 14:38, 29 October 2010 diff hist +867 N BamUtil: trimBam Created page with '== Trim BAM == The <code>trimBam</code> program is released as part of the StatGen Library & Tools download. <code>trimBam</code> trims the end of reads in a SAM/BAM file, chang…'
- 13:33, 29 October 2010 diff hist 0 C++ Library: libStatGen
- 13:33, 29 October 2010 diff hist +843 C++ Library: libStatGen
- 19:10, 25 October 2010 diff hist +42 N C++ Library: libStatGen Created page with 'To use the StatGenLibrary, first download:'
- 12:02, 25 October 2010 diff hist +207 FastQValidator
- 11:47, 25 October 2010 diff hist +35 N C++ Library: libfqf moved C++ Library: libfqf to StatGenLibrary: FASTQ current
- 11:47, 25 October 2010 diff hist 0 m LibStatGen: FASTQ moved C++ Library: libfqf to StatGenLibrary: FASTQ
- 11:42, 25 October 2010 diff hist +33 N C++ Library: libbam moved C++ Library: libbam to StatGenLibrary: BAM current
- 11:42, 25 October 2010 diff hist 0 m LibStatGen: BAM moved C++ Library: libbam to StatGenLibrary: BAM
- 13:01, 13 October 2010 diff hist -136 BamUtil: filter
- 13:00, 13 October 2010 diff hist -643 BamUtil
- 12:58, 13 October 2010 diff hist -721 BamUtil: validate
- 12:57, 13 October 2010 diff hist +520 BamUtil
- 12:15, 11 October 2010 diff hist -1 C++ Class: CigarRoller →Cigar
- 11:58, 8 October 2010 diff hist -3,136 Sam Library Usage Examples
- 17:29, 30 September 2010 diff hist +2,583 BamUtil: filter
- 17:11, 30 September 2010 diff hist +1,364 BamUtil: filter
- 16:30, 30 September 2010 diff hist +129 BamUtil: filter
- 16:29, 30 September 2010 diff hist +575 BamUtil: filter
- 16:24, 30 September 2010 diff hist +698 BamUtil: filter
- 15:58, 30 September 2010 diff hist +408 BamUtil: filter
- 15:55, 30 September 2010 diff hist +637 BamUtil: filter
- 15:51, 30 September 2010 diff hist +1,175 BamUtil: filter
- 15:18, 30 September 2010 diff hist +1,247 N BamUtil: filter Created page with 'Category:libbam == filter == The <code>filter</code> option on the bam executable writes the alignments filtering them by clipping ends with too high of a mismatch …'
- 15:15, 30 September 2010 diff hist +585 BamUtil
- 15:05, 30 September 2010 diff hist +271 BamUtil
- 15:01, 30 September 2010 diff hist +1,033 BamUtil
- 11:34, 30 September 2010 diff hist +100 BamUtil
- 18:52, 29 September 2010 diff hist +39 LibStatGen: BAM
- 18:44, 29 September 2010 diff hist +147 N Category:C++ Created page with 'If you create a page for C++ software, add <pre>Category:C++</pre> to the bottom of the page so that it will automatically be included here.' current
- 18:37, 29 September 2010 diff hist +129 C++ Class: CigarRoller →Public Methods
- 18:36, 29 September 2010 diff hist +11 C++ Class: CigarRoller →Public Methods
- 18:35, 29 September 2010 diff hist +135 C++ Class: CigarRoller →Public Methods
- 18:08, 29 September 2010 diff hist +14 C++ Class: CigarRoller →static Methods
- 18:08, 29 September 2010 diff hist +568 C++ Class: CigarRoller
- 18:05, 29 September 2010 diff hist +3 C++ Class: CigarRoller →Public Methods
- 18:04, 29 September 2010 diff hist +151 C++ Class: CigarRoller →Public Methods
- 18:03, 29 September 2010 diff hist +147 LibStatGen: general
- 17:50, 29 September 2010 diff hist -22 C++ Class: InputFile
- 17:50, 29 September 2010 diff hist -22 C++ Class: CigarRoller
- 17:48, 29 September 2010 diff hist +156 N Category:Libcsg Created page with 'If you create a page for software in libcsg, add <pre>Category:libcsg</pre> to the bottom of the page so that it will automatically be included here.' current
- 17:47, 29 September 2010 diff hist +61 C++ Class: CigarRoller
- 17:46, 29 September 2010 diff hist +61 LibStatGen: general
- 17:45, 29 September 2010 diff hist +60 C++ Class: InputFile
- 17:44, 29 September 2010 diff hist +978 C++ Library: general Change Log
- 17:28, 29 September 2010 diff hist +201 C++ Class: InputFile
- 17:26, 29 September 2010 diff hist +434 C++ Class: InputFile →Example
- 17:21, 29 September 2010 diff hist +2,197 C++ Class: InputFile
- 16:12, 29 September 2010 diff hist +27 C++ Class: InputFile →InputFile / IFILE
- 17:25, 21 September 2010 diff hist +346 SAM: Filtering Reads current
- 17:20, 21 September 2010 diff hist +3,316 N SAM: Filtering Reads Created page with 'Two filters have been requested for updating a SAM/BAM File. A program should be written that will run both at the same time and produce an updated SAM/BAM File. # Sum the qual…'
- 14:55, 20 September 2010 diff hist +32 BAM Review Action Items →Notes
- 14:45, 20 September 2010 diff hist +92 BAM Review Action Items
- 14:25, 20 September 2010 diff hist +319 BAM Review Action Items →Accessing String Values
- 14:10, 20 September 2010 diff hist +38 BAM Review Action Items
- 15:42, 17 September 2010 diff hist +156 BAM Review Action Items →NOTES From Meeting
- 15:30, 17 September 2010 diff hist -23 BAM Review Action Items
- 13:43, 17 September 2010 diff hist +251 BAM Review Action Items
- 13:00, 17 September 2010 diff hist +382 BAM Review Action Items →Accessing String Values
- 12:42, 17 September 2010 diff hist +313 BAM Review Action Items
- 12:32, 17 September 2010 diff hist -1 BamUtil →Usage
- 12:27, 17 September 2010 diff hist +93 BAM Review Action Items →Review Sept 17th
- 12:17, 17 September 2010 diff hist +1 BAM Review Action Items
- 10:16, 17 September 2010 diff hist +3,889 BAM Review Action Items
- 09:50, 17 September 2010 diff hist +200 BAM Review Action Items
- 09:43, 17 September 2010 diff hist +37 BAM Review Action Items
- 09:43, 17 September 2010 diff hist +1,684 BAM Review Action Items
- 08:36, 17 September 2010 diff hist +52 BAM Review Action Items
- 15:51, 27 August 2010 diff hist +258 SAM Validation Criteria current
- 10:38, 26 August 2010 diff hist +70 C++ Class: SamFile →Statistic Generation
- 17:22, 23 August 2010 diff hist +293 C++ Class: SamFile
- 17:20, 23 August 2010 diff hist -1 C++ Class: SamFile
- 17:19, 23 August 2010 diff hist +336 C++ Class: SamFile →Statistic Generation
- 17:00, 23 August 2010 diff hist +183 BamUtil: validate
- 16:59, 23 August 2010 diff hist +69 C++ Class: SamFile →Statistics
- 14:34, 23 August 2010 diff hist -2,504 BamUtil: validate
- 14:33, 23 August 2010 diff hist +2,597 C++ Class: SamFile
- 09:00, 11 August 2010 diff hist +1,620 C++ Class: CigarRoller
- 08:39, 11 August 2010 diff hist -12 SAM/BAM Classes FAQs
- 08:38, 11 August 2010 diff hist +307 C++ Library: general Change Log
- 08:35, 11 August 2010 diff hist +307 C++ Class: SamRecord
- 08:32, 11 August 2010 diff hist +668 C++ Class: SamRecord
- 08:19, 11 August 2010 diff hist +378 C++ Class: SamFile
- 11:11, 4 August 2010 diff hist +70 CigarRoller Proposed Update current
- 11:03, 4 August 2010 diff hist +261 CigarRoller Proposed Update →How would this be used by SamRecord
- 11:00, 4 August 2010 diff hist +634 CigarRoller Proposed Update
- 10:52, 4 August 2010 diff hist +3,995 N CigarRoller Proposed Update Created page with '* Should we rename CigarRoller to Cigar? * Should we be consistent in upper-case vs lower-case first letter of method names? * Should Cigar require a start position? ** I would l…'
- 16:39, 3 August 2010 diff hist +211 C++ Class: CigarRoller
- 16:36, 3 August 2010 diff hist +1,449 C++ Class: CigarRoller
- 13:19, 3 August 2010 diff hist +983 C++ Class: CigarRoller
- 12:49, 3 August 2010 diff hist +14 BAM Review Action Items
- 12:47, 3 August 2010 diff hist +206 C++ Class: SamFile
- 11:51, 3 August 2010 diff hist +1,016 C++ Class: CigarRoller →Mapping Between Reference and Read/Query
- 11:39, 3 August 2010 diff hist +997 C++ Class: CigarRoller
- 11:22, 3 August 2010 diff hist +428 C++ Library: general Change Log
- 12:27, 2 August 2010 diff hist +2,075 N C++ Class Averages Created page with '<source lang="cpp"> // Static method that returns the mean, meadian, and mode for this dataset. void Average::calculateAverages(double& mean, doub…' current
- 11:37, 2 August 2010 diff hist +358 C++ Class: CigarRoller
- 11:33, 2 August 2010 diff hist +84 SAM/BAM Classes FAQs
- 11:32, 2 August 2010 diff hist +63 SAM/BAM Classes FAQs
- 10:44, 2 August 2010 diff hist +134 SAM/BAM Classes FAQs
- 10:42, 2 August 2010 diff hist +4,961 Sam Library Usage Examples
- 17:55, 30 July 2010 diff hist +1 Introduction to new students →Data File Formats
- 17:54, 30 July 2010 diff hist +165 Introduction to new students →Data File Formats
- 17:53, 30 July 2010 diff hist +45 Introduction to new students →Data File Formats
- 17:52, 30 July 2010 diff hist +92 Introduction to new students →Data File Formats
- 17:50, 30 July 2010 diff hist +96 Introduction to new students →Resources
- 17:39, 30 July 2010 diff hist +3,335 SAM
- 16:26, 30 July 2010 diff hist +403 SAM
- 13:43, 30 July 2010 diff hist -122 SAM
- 13:38, 30 July 2010 diff hist +38 SAM
- 13:34, 30 July 2010 diff hist +313 SAM
- 13:12, 30 July 2010 diff hist +118 SAM
- 11:48, 30 July 2010 diff hist +647 SAM
- 11:05, 30 July 2010 diff hist 0 SAM
- 11:05, 30 July 2010 diff hist +96 SAM
- 17:49, 29 July 2010 diff hist +1,063 SAM/BAM Classes FAQs
- 17:35, 29 July 2010 diff hist +4 C++ Class: SamFile
- 17:26, 29 July 2010 diff hist +8 SAM/BAM Classes FAQs
- 17:25, 29 July 2010 diff hist +6 SAM/BAM Classes FAQs
- 17:23, 29 July 2010 diff hist +339 N SAM/BAM Classes FAQs Created page with '== How Do I? == * Map between a query/read sequence and a reference sequence to do things like looking up a base/quality at a given reference position or looking up a reference …'
- 17:18, 29 July 2010 diff hist +37 LibStatGen: BAM
- 17:16, 29 July 2010 diff hist +1,593 C++ Class: CigarRoller
- 14:34, 29 July 2010 diff hist -1 SAM →What Information Does SAM/BAM Have for an Alignment
- 14:32, 29 July 2010 diff hist -1 SAM
- 14:32, 29 July 2010 diff hist +1,394 SAM
- 14:13, 29 July 2010 diff hist +142 SAM
- 13:31, 29 July 2010 diff hist +475 SAM
- 11:51, 29 July 2010 diff hist +2,359 SAM
- 11:15, 29 July 2010 diff hist +2,373 SAM
- 16:17, 28 July 2010 diff hist +18 BamUtil
- 16:17, 28 July 2010 diff hist +18 BamUtil →readIndexedBam
- 16:17, 28 July 2010 diff hist +832 BamUtil
- 14:49, 23 July 2010 diff hist +117 Software →Validators
- 11:24, 22 July 2010 diff hist -6 BamUtil: validate